Investigating respiratory rhythm generation using photoacoustic imaging

Host laboratory and collaborators


Breathing is a continuous oscillatory activity, driven by a complex neuronal network deep in the brain. Core to this network is a group of neurons that generates the respiratory rhythm, yet we still lack fundamental understanding about how it works in an integrated and physiological condition. Recording the activity of the neurons involved using now conventional high resolution imaging techniques, such as 2-photon microscopy, is impossible due to the depth of these neurons in the brain tissue. With this project, we aim at developing a photoacoustic imaging setup, able to image non-invasively in deep soft tissue (>2 mm). We will use an integrated in situ preparation (“Working Heart-Brainstem Preparation”) that enables recordings of physiological neuronal and nervous respiratory activities, while providing a controllable set-up ideal to develop and fine tune our photoacoustic imaging approach. We will use 1-photon microendoscopic calcium imaging, the current reference system for deep brain imaging, as control experiments.


Photoacoustic imaging; deep neuronal circuits imaging; respiratory rhythm generation; functional micronetwork dynamics; technological breakthrough.


The successful applicant will first learn (at Inmed) (i) how to do stereotaxic injections of virus (for expression of calcium indicators and optogenetic tools) in respiratory neuronal groups in the brainstem of juvenile rats, and (ii) how to run the Working Heart-Brainstem Preparation. Then, 1-photon microendoscopic calcium imaging of respiratory neurons will be performed, and in parallel the successful applicant will learn (at Institut Fresnel) how to perform photoacoustic imaging using a cutting edge all-optical setup, in order to record calcium activity from respiratory neurons.

Expected profile

We are looking for a highly motivated candidate with a PhD in neuroscience, biophysics, or similar. Previous experience in electrophysiology, signal processing and programming are required. Previous experience with stereotaxic injection of viruses, calcium imaging, optogenetics, and/or the Working Heart-Brainstem Preparation, would be a plus but is not compulsory.

Articles related to the project

[1] E. Zhang, J. Laufer, and P. Beard, “Backward-mode multiwavelength photoacoustic scanner using a planar Fabry-Perot polymer film ultrasound sensor for high-resolution three-dimensional
imaging of biological tissues,” Appl. Opt., AO, vol. 47, no. 4, pp. 561–577, 2008, 10.1364/AO.47.000561.

[2] X. L. Deán-Ben et al., “Functional optoacoustic neuro-tomography for scalable whole-brain monitoring of calcium indicators,” Light: Science & Applications, vol. 5, no. 12, p. e16201, 2016,

[3] J.M. Ramirez and N.A. Baertsch, “The dynamic basis of respiratory rhythm generation: one breath at a time”, Annu. Rev. Neurosci., 41, 475-499, 2018, 10.1146/annurev-neuro-080317-061756.

[4] J.F. Paton, “The ventral medullary respiratory network of the mature mouse studied in a working heart-brainstem preparation”, J. Physiol., Jun 15;493, (Pt 3) 819-31, 1996, 10.1113/jphysiol.1996.sp021425.